artmsEvidenceToSAINTq: MaxQuant evidence file to SAINTq format

In kroganlab/artMS: Analytical R tools for Mass Spectrometry

MaxQuant evidence file to SAINTq format

Description

Converts the MaxQuant evidence file to the required files by SAINTq. The user can choose to use either peptides with ⁠spectral counts⁠ (use msspc) or the all the peptides (use all) for the analysis. The quantitative can be also chosen (either MS Intensity or Spectral Counts)

Usage

artmsEvidenceToSAINTq(
  evidence_file,
  keys_file,
  output_dir = "artms_saintq",
  sc_option = c("all", "msspc"),
  fractions = FALSE,
  quant_variable = c("msint", "msspc"),
  verbose = TRUE
)

Arguments

evidence_file	(char or data.frame) The evidence file path and name, or data.frame
keys_file	(char) Keys file with a SAINT column specifying test (T) and control (C) conditions
output_dir	(char) New directory to create and save files. Default is current directory (recommended to provide a new folder name).
sc_option	(char). Filter peptides with spectral counts only. Two options: msspc: use only peptides with spectral_counts all (default): all peptides detected (including the one resulting from the MaxQuant 'Match between run' algorithm)
fractions	(logical) TRUE for 2D proteomics (fractions). Default: FALSE
quant_variable	(char) Select the quantitative variable. Two options available: msint: MS Intensity (default) msspc: MS.MS.count (Spectral Counts)
verbose	(logical) TRUE (default) shows function messages

Details

After running the script, the new specified folder should contain the folling files:

• saintq-config-peptides

• saintq-config-proteins

• saintq_input_peptides.txt

• saintq_input_proteins.txt

Then cd into the new folder and run either of the following two options (assuming that saintq is installed in your linux/unix/mac os x system):

⁠> saintq config-saintq-peptides⁠

or

⁠> saintq config-saintq-proteins⁠

Value

The input files requires to run SAINTq

Examples

# Testing that the files cannot be empty
artmsEvidenceToSAINTq   (evidence_file = NULL, 
                                   keys_file = NULL, 
                                   output_dir = NULL)

kroganlab/artMS documentation built on July 7, 2023, 5:35 a.m.